# HG changeset patch
# User bgruening
# Date 1408024659 14400
# Node ID bb468ee178d8be3eef39b18aa2e8211fa5a71d0a
# Parent  4ffcf0672e81dbd6fcd8c60b967b9470db03f7d3
Uploaded

diff -r 4ffcf0672e81 -r bb468ee178d8 vt_normalize.xml
--- a/vt_normalize.xml	Thu Aug 14 07:40:02 2014 -0400
+++ b/vt_normalize.xml	Thu Aug 14 09:57:39 2014 -0400
@@ -11,7 +11,7 @@
         vt @BINARY@
             -o "${ outfile }"
             ##-q  do not print options and summary []
-            -w  window size for local sorting of variants [10000]
+            -w $window
 
             #if str( $intervals_file ) != 'None':
                 -I  "${intervals_file}"
@@ -20,7 +20,7 @@
             ##-i  intervals []
 
             #if $reference_source.reference_source_selector != "history":
-                -r "${reference_source.reference_genome.fields.path}"'
+                -r "${reference_source.reference_genome.fields.path}"
             #else:
                 -r "${reference_source.reference_genome}"
             #end if